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            "License :: OSI Approved :: BSD License",
            "Operating System :: MacOS",
            "Operating System :: Microsoft :: Windows",
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            "Programming Language :: Python :: 3.6",
            "Programming Language :: Python :: 3.7",
            "Programming Language :: Python :: 3.8",
            "Programming Language :: Python :: 3.9",
            "Topic :: Scientific/Engineering :: Bio-Informatics",
            "Topic :: Utilities"
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        "description": "# kb-python\n![github version](https://img.shields.io/badge/Version-0.27.2-informational)\n[![pypi version](https://img.shields.io/pypi/v/kb-python)](https://pypi.org/project/kb-python/0.27.2/)\n![python versions](https://img.shields.io/pypi/pyversions/kb_python)\n![status](https://github.com/pachterlab/kb_python/workflows/CI/badge.svg)\n[![codecov](https://codecov.io/gh/pachterlab/kb_python/branch/master/graph/badge.svg)](https://codecov.io/gh/pachterlab/kb_python)\n[![pypi downloads](https://img.shields.io/pypi/dm/kb-python)](https://pypi.org/project/kb-python/)\n[![docs](https://readthedocs.org/projects/kb-python/badge/?version=latest)](https://kb-python.readthedocs.io/en/latest/?badge=latest)\n[![license](https://img.shields.io/pypi/l/kb-python)](LICENSE)\n\nkb-python is a python package that wraps the [kallisto | bustools](https://www.kallistobus.tools) single-cell RNA-seq workflow [2]. It was developed by Kyung Hoi (Joseph) Min and A. Sina Booeshaghi.\n\nThe wrapper simplifies downloading and running of the kallisto\n[1] and bustools [2] programs. It was inspired by Sten Linnarsson\u2019s `loompy\nfromfq` command (http://linnarssonlab.org/loompy/kallisto/index.html)\n\nThe `kb` program consists of two parts:\n\nThe `kb ref` command builds or downloads a species-specific index for\npseudoalignment of reads. This command must be run prior to `kb count`, and it\nruns the `kallisto index` [1].\n\nThe `kb count` command runs the kallisto [1] and bustools [2] programs. It can\nbe used for pre-processing of data from a variety of single-cell RNA-seq\ntechnologies, and for a number of different workflows (e.g. production of gene\ncount matrices, RNA velocity analyses, etc.). The output can be saved in a\nvariety of formats including mtx and loom.\n\nIf you use `kb` we ask that you cite the following two papers:\n\n[1] Bray, N. L., Pimentel, H., Melsted, P., & Pachter, L. (2016). Near-optimal\nprobabilistic RNA-seq quantification.\u00a0Nature biotechnology,\u00a034(5), 525.\n\n[2] Melsted, P., Booeshaghi, A. S., Liu, L., Gao, F., Lu, L., Min, K. H., da Veiga Beltrame, E., Hjorleifsson, K. E., Gehring, J., & Pachter, L. (2021). Modular and efficient pre-processing of single-cell RNA-seq. Nature Biotechnology.\n\n## Prerequisites\nNone. The kallisto and bustools binaries are included with the package.\n\n## Documentation\n- User documentation and tutorials are available [here](https://www.kallistobus.tools).\n- Developer documentation is hosted on [Read the Docs](https://kb-python.readthedocs.io/en/latest/).",
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